aaDistribution: Amino acid distribution of sequences

Description

This function calculates the amino acid distribution of sequences. Distribution is calculated for sequences of the same length and therein for each position. aaDistribution returns a list containing either only amino acid distribution or a list containing amino acid distribution and analyzed number of sequences per length. plotAADistribution visualizes the amino acid distribution of sequences of the same length.

Usage

aaDistribution(sequences = NULL, numberSeq = FALSE)

plotAADistribution(aaDistribution.tab=NULL, plotSeqN=FALSE, 
     PDF=NULL, ...)

Arguments

sequences

A vector containing amino acid sequences.

numberSeq

TRUE: table containing number of sequences will be returned, as well (default: FALSE).

aaDistribution.tab

Output list of function aaDistribution()

plotSeqN

TRUE: Number of sequences for each length will be plotted (see Details; default: FALSE).

PDF

PDF project name (see Details)

...

Value

Output is a list containing
Amino_acid_distributionlist contains data frames of amino acid distributions for each length
Number_of_sequences_per_lengthdata frame contains the number of sequences for each length, used for analysis (optional)

Details

The vector containing sequences will be divided in sequences of the same length and then amino acid distribution for each position is done. If numberSeq = T, the number of sequences used for the analysis of sequences of the same length will be returned, as well. This information is also required for

plotAADistribution(..., 
plotSeqN = T)

. In the plot sequence numbers equal to 0 are not plotted; smallest number is 1. The PDF character string should be only the project name (without ".pdf"). If plotAADistr = T a figure called "PDF"_Amino-acid-distribution.pdf will be saved to your working directory. If plotSeqN = T a figure called "PDF"_Number-of-sequences.pdf will be saved.

Examples

Run this code

data(aaseqtab)
aadistr<-aaDistribution(sequences = aaseqtab$CDR3_IMGT, numberSeq = TRUE)
plotAADistribution(aaDistribution.tab=aadistr, plotAADistr=TRUE, plotSeqN=FALSE, 
     PDF="test")